Genomic epidemiology of urogenital-associated Neisseria meningitidis isolates from gonorrhea high-risk populations in China

Although Neisseria meningitidi s ( N. meningitidis ) is classically associated with invasive meningococcal disease, it has emerged as an underrecognized cause of urethritis among populations at increased risk for gonorrhea. Because urogenital N. meningitidis infection can clinically resemble gonococcal urethritis and may not be routinely identified, epidemiologically important lineages and antimicrobial resistance (AMR)-associated determinants may remain underrecognized. Such infections have been sporadically reported in China, but their genomic diversity, evolutionary relationships, and AMR characteristics remain poorly characterized. Fourteen N. meningitidis isolates collected from urethral and pharyngeal specimens in Shanghai and Guangzhou were analyzed using antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS), and phylogenetic analysis. Pan-genome and recombination analyses were further performed to characterize genomic variation and investigate the evolutionary patterns of the predominant lineages, ST-1466 and ST-11,026. Among the 14 isolates (10 urogenital and 4 pharyngeal), six distinct STs were identified, with ST-1466 (6/14) and ST-11,026 (3/14) predominating. The Chinese urogenital ST-1466 isolates clustered within the North American lineage (Cluster B) but displayed an AMR profile more similar to those of Cluster A isolates. Recombination analysis identified lineage-specific genomic regions in ST-1466, including loci involved in iron acquisition and metabolism. The Chinese and Japanese urogenital ST-11,026 isolates formed a closely related cluster and were resistant to ciprofloxacin (CIP), whereas the urogenital ST-3200 isolate clustered with other Chinese isolates. Most isolates were resistant to penicillin (PEN) and trimethoprim–sulfamethoxazole (SXT). Notably, one pharyngeal isolate showed reduced susceptibility to third-generation cephalosporins and harbored the rare pen 842 allele. Urogenital-associated N. meningitidis lineages may be circulating in China, with some isolates being genetically related to internationally reported lineages and carrying AMR-associated determinants. Recombination involving genes related to iron acquisition and metabolism may reflect ongoing genomic diversification, although its contribution to urogenital adaptation requires functional validation. These findings highlight the importance of strengthened genomic surveillance and routine AST of N. meningitidis isolates recovered from urogenital infections.